renalware-core 2.0.145 → 2.0.151

data/config/initializers/wicked_pdf.rb

@@ -20,3 +20,15 @@ WickedPdf.config = {
   # (but can be overridden in `render :pdf` calls)
   # layout: 'pdf.html',
 }
+
+# This is a hack to get ViewComponent and WickedPDF to work together.
+# See https://github.com/github/view_component/issues/288
+# Basically in Rails 5.x, both gems monkey patch ActionView render_to_string
+# and we can get an infinite loop when rendering PDFs.
+# Once we move to Rails 6 I think think this can be removed
+class WickedPdf
+  module PdfHelper
+    remove_method(:render_to_string)
+    remove_method(:render)
+  end
+end

data/config/locales/en-GB.yml

@@ -39,7 +39,7 @@ en-GB:
     - Saturday
     formats:
       default: "%d-%b-%Y"
-      long: "%a %e %b %Y"
+      long: "%a %d %b %Y"
       short: "%d %b"
       compact: "%d-%b-%y"
     month_names:

data/config/locales/renalware/events/advanced_care_plan.en.yml

@@ -0,0 +1,12 @@
+en:
+  renalware/events/advanced_care_plan:
+    title: "Advanced Care Plans"
+    description_column_title: State
+  enumerize:
+    renalware/events/advanced_care_plan/document:
+      state:
+        not_required: "ACP not required"
+        required_but_not_started: "ACP required but not started"
+        acp_in_progress: "ACP in progress"
+        acp_complete: "ACP complete"
+        acp_declined: "ACP declined"

data/config/locales/renalware/events/biopsy.en.yml

@@ -1,4 +1,6 @@
 en:
+  renalware/events/biopsy:
+    title: "Biopsies"
   activemodel:
     attributes:
       renalware/events/biopsy/document:

data/config/locales/renalware/events/clinical_frailty_score.en.yml

@@ -0,0 +1,16 @@
+en:
+  renalware/events/clinical_frailty_score:
+    title: "Clinical Frailty Scores"
+    description_column_title: Score
+  enumerize:
+    renalware/events/clinical_frailty_score/document:
+      score:
+        1: 1
+        2: 2
+        3: 3
+        4: 4
+        5: 5
+        6: 6
+        7: 7
+        8: 8
+        9: 9

data/config/locales/renalware/events/clinical_frailty_score_component.en.yml

@@ -0,0 +1,8 @@
+en:
+  renalware:
+    events:
+      clinical_frailty_score_component:
+        date_time: Date time
+        score: Score
+        created_at: Created
+        created_by: By

data/config/locales/renalware/medications/prescription.yml

@@ -14,7 +14,8 @@ en:
         terminated_on: Terminated on
         frequency: "Frequency & Duration"
         administer_on_hd: Give on HD
-        last_delivery_date: Last delivery date
+        last_delivery_date: Last home prescription date
+        next_delivery_date: Next home prescription date
     errors:
       models:
         renalware/medications/prescription:

data/config/locales/renalware/navigation/renal.en.yml

@@ -12,6 +12,7 @@ en:
         hd_patients_with_unmet_preferences: HD Patients with un-met preferences
         letters: Letters
         esa_prescriptions: ESA Patients
+        home_delivery_prescriptions: Home Delivery Prescriptions
         audits: Audits
         aki_alerts: AKI Alerts
         studies: Clinical Studies

data/config/locales/renalware/nhs_number.en.yml

@@ -0,0 +1,6 @@
+en:
+  activerecord:
+    errors:
+      messages:
+        nhs_number_invalid_checkdigit: "is invalid - please check"
+        nhs_number_not_numeric: "is invalid -  must be 10 digits"

data/config/locales/renalware/pd/adequacy_result.en.yml

@@ -0,0 +1,9 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/adequacy_result:
+        dial_24_vol_in: Dial 24 vol in (ml)
+        dial_24_vol_out: Dial 24 vol out (ml)
+        urine_24_vol: Urine 24 vol (ml)
+        height: Height (m)
+        weight: Weight (kg)

data/config/locales/renalware/pd/dashboard.en.yml

@@ -8,6 +8,9 @@ en:
             add_capd_regime: CAPD Regime
             add_apd_regime: APD Regime
             add_pet_adequacy: PET Adequacy
+            add_unified_pet_adequacy: PET & Adequacy
+            add_pet: PET
+            add_adequacy: Adequacy
             add_exit_site_infection: Exit Site Infection
             add_peritonitis_episode: Peritonitis Episode
             add_pd_assessment: PD Assessment

data/config/locales/renalware/pd/pet_result.en.yml

@@ -0,0 +1,23 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/pet_result:
+        net_uf: PET_netUF
+        d_pcr: PET_D_Pcr
+        dextrose_concentration: Dextrose
+        dextrose_concentration_id: Dextrose
+        volume_in: Volume in (ml)
+        volume_out: Volume out (ml)
+        infusion_time: Infusion time (min)
+        drain_time: Drain time (min)
+        overnight_dextrose_concentration: Overnight dextrose
+        overnight_dextrose_concentration_id: Overnight dextrose
+        overnight_volume_in: Overnight vol in (ml)
+        overnight_volume_out: Overnight vol out (ml)
+        overnight_dwell_time: Overnight dwell time (min)
+
+  enumerize:
+    renalware/pd/pet_result:
+      pet_type:
+        fast: Fast
+        full: Full

data/config/locales/renalware/renal/registry.en.yml

@@ -8,3 +8,4 @@ en:
           comorbidities_at_esrf: Comorbidities
           first_seen_on: Date first seen
           cause_of_death: Cause of death
+          esrf: ESRF

data/config/routes/admin.rb

@@ -3,6 +3,11 @@
 namespace :admin do
   resources :users
   resource :dashboard, only: :show
+  resource :playground, only: :show do
+    scope constraints: { format: :json } do
+      get :pathology_chart_data
+    end
+  end
   namespace :feeds do
     resources :files, only: [:index, :show, :new, :create]
   end

data/config/routes/letters.rb

@@ -22,6 +22,11 @@ resources :patients, only: [] do
 end
 
 namespace :letters do
+  resources :mailshots, only: [:create, :new, :index], controller: "mailshots/mailshots"
+  namespace :mailshots do
+    resources :patient_previews, only: :index
+  end
+
   resources :batches, only: [:create, :index, :show] do
     get :status, constraints: { format: :json }, defaults: { format: :json }
     resources :completions, only: [:new, :create], controller: "completed_batches"

data/config/routes/medications.rb

@@ -22,4 +22,9 @@ namespace :medications do
             only: :index,
             drug_type_name: :esa,
             controller: "drug_types/prescriptions"
+  namespace :home_delivery do
+    constraints(named_filter: /#{Renalware::Medications::Delivery::DRUG_TYPE_FILTERS.join("|")}/) do
+      get "prescriptions/:named_filter", to: "prescriptions#index", as: :prescriptions
+    end
+  end
 end

data/config/routes/pathology.rb

@@ -2,6 +2,7 @@
 
 resources :patients, only: [] do
   namespace :pathology do
+    resources :charts, only: [:show]
     get "observations/current",
         to: "current_observation_results#index",
         as: "current_observations"
@@ -11,6 +12,11 @@ resources :patients, only: [] do
     get "observations/historical",
         to: "historical_observation_results#index",
         as: "historical_observations"
+    scope constraints: { format: :json, date: /\d{4}-\d{2}-\d{2}/ } do
+      get "observations/nearest/code_group/:code_group_id/date/:date",
+          to: "nearest_observation_results#index",
+          as: "nearest_observations"
+    end
     resources :observation_requests, only: [:index, :show]
     resources :patient_rules
     get "descriptions/:description_id/observations",

data/config/routes/patients.rb

@@ -27,7 +27,7 @@ resources :patients, except: [:destroy], controller: "patients/patients" do
   resource :death, only: [:edit, :update]
   resource :primary_care_physician,
            controller: "patients/primary_care_physician",
-           only: [:edit, :update]
+           only: [:edit, :update, :destroy]
 
   resources :bookmarks, only: :create, controller: "patients/bookmarks"
   resources :alerts, only: [:new, :create, :destroy], controller: "patients/alerts"

data/config/routes/pd.rb

@@ -15,6 +15,9 @@ resources :patients, only: [] do
     resources :peritonitis_episodes, only: [:new, :create, :show, :edit, :update]
     resources :exit_site_infections, only: [:new, :create, :show, :edit, :update]
     resources :pet_adequacy_results, except: [:destroy]
+    resources :unified_pet_adequacies, only: [:new, :create]
+    resources :pet_results
+    resources :adequacy_results
     resources :assessments, except: [:index, :destroy]
     resources :training_sessions, except: [:index, :destroy]
     resource :mdm, only: :show, controller: "mdm"
@@ -22,6 +25,8 @@ resources :patients, only: [] do
 end
 
 namespace :pd do
+  resources :pet_completions, only: :index
+  resources :adequacy_completions, only: :index
   resources :bag_types, except: [:show]
   resources :infection_organisms
   resources :mdm_patients, only: :index

data/config/routes/renal.rb

@@ -12,6 +12,7 @@ namespace :renal do
     collection do
       get :patients
       get :deaths
+      get :missing_esrf
     end
   end
 end

data/config/routes/system.rb

@@ -25,7 +25,8 @@ devise_for :users,
 
 # An ajax-polled route which will cause the users browser to redirect to the login page
 #  when their session expires
-get "/session_timed_out" => "session_timeout#has_user_timed_out", as: "session_timed_out"
+get "/check_session_expired" => "session_timeout#check_session_expired", as: "check_session_expired"
+get "/keep_session_alive" => "session_timeout#keep_session_alive", as: "keep_session_alive"
 
 super_admin_constraint = lambda do |request|
   current_user = request.env["warden"].user || Renalware::NullUser.new

data/db/functions/generate_secure_id_v01.sql

@@ -9,7 +9,7 @@ CREATE OR REPLACE FUNCTION generate_secure_id(length integer default 24)
   */
   RETURNS text AS
   $body$
-  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789',
+  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ9999999999',
                      ceil (random() * 62)::integer,
                      1), '')
   FROM   generate_series(1, length)

data/db/functions/pathology_chart_data_v01.sql

@@ -0,0 +1,13 @@
+/* Returns a table of date => result for a patient, obx code (eg HGB) and start date */
+CREATE OR REPLACE FUNCTION renalware.pathology_chart_data(patient_id integer, code text, start_date date)
+ RETURNS TABLE(observed_on date, result float)
+ LANGUAGE sql
+AS $function$
+   SELECT observed_at::date, convert_to_float(result) from pathology_observations po
+   inner join pathology_observation_requests por on por.id = po.request_id
+   inner join pathology_observation_descriptions pod on pod.id = po.description_id
+   where pod.code = $2 and observed_at >= start_date and por.patient_id = $1
+   order by po.observed_at asc, po.created_at desc;
+
+$function$
+;

data/db/migrate/20200226145010_add_unique_indexes.rb

@@ -0,0 +1,46 @@
+class AddUniqueIndexes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      # Allow only one transplant_registration per patient
+      remove_index :transplant_registrations, :patient_id
+      add_index :transplant_registrations, :patient_id, unique: true
+
+      # Allow only one un-terminated transplant_registration_status per patient
+      # Removed this for now as the way we update the terminated_on in the model
+      # prevents us from enforcing this constraint atm.
+      # remove_index :transplant_registration_statuses, :registration_id
+      # add_index(
+      #   :transplant_registration_statuses,
+      #   :registration_id,
+      #   unique: true,
+      #   where: "terminated_on is null"
+      # )
+
+      # Allow only one current modality_modalities per patient
+      add_index(
+        :modality_modalities,
+        :patient_id,
+        unique: true,
+        where: "ended_on is null",
+        name: :index_modality_modalities_on_patient_id_current
+      )
+
+      # Removed this for now as prevents adding new profiles. Need to address holistically in
+      # a separate PR
+      # # An access profile must have a start date
+      # change_column_null :access_profiles, :started_on, false
+      # # Allow only on unterminated access profile per patient
+      # add_index(
+      #   :access_profiles,
+      #   :patient_id,
+      #   unique: true,
+      #   where: "terminated_on is null",
+      #   name: :index_access_profiles_on_patient_id_current
+      # )
+
+      # Allow only one renal_profile per patient
+      remove_index :renal_profiles, :patient_id
+      add_index :renal_profiles, :patient_id, unique: true
+    end
+  end
+end

data/db/migrate/20200313120655_create_pathology_chart_data_function.rb

@@ -0,0 +1,13 @@
+class CreatePathologyChartDataFunction < ActiveRecord::Migration[5.2]
+  def up
+    within_renalware_schema do
+      load_function("pathology_chart_data_v01.sql")
+    end
+  end
+
+  def down
+    within_renalware_schema do
+      connection.execute("DROP FUNCTION IF EXISTS pathology_chart_data(integer, text, date);")
+    end
+  end
+end

data/db/migrate/20200318134807_create_letter_mailshots.rb

@@ -0,0 +1,50 @@
+class CreateLetterMailshots < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table(
+        :letter_mailshot_mailshots,
+        comment: "A mailshot is an adhoc letter sent to a group of patients"
+      ) do |t|
+        t.string(
+          :description,
+          null: false,
+          comment: "Some text to identify the mailshot purpose. "\
+                   "Will be written to letter_letters.description column when letter created"
+        )
+        t.string(
+          :sql_view_name,
+          null: false,
+          comment: "The name of the SQL view chosen as the data source"
+        )
+        t.text(
+          :body,
+          null: false,
+          comment: "The body text that will be inserted into each letter"
+        )
+        t.references :letterhead, foreign_key: { to_table: :letter_letterheads }, null: false
+        t.references :author, foreign_key: { to_table: :users }, index: true, null: false
+        t.integer :letters_count, comment: "Counter cache column which Rails will update"
+        t.references :created_by, foreign_key: { to_table: :users }, null: false
+        t.references :updated_by, foreign_key: { to_table: :users }, null: false
+        t.timestamps null: false
+      end
+
+      # rubocop:disable Rails/CreateTableWithTimestamps
+      create_table(
+        :letter_mailshot_items,
+        comment: "A record of the letters sent in a mailshot"
+      ) do |t|
+        t.references :mailshot, foreign_key: { to_table: :letter_mailshot_mailshots }, null: false
+        t.references :letter, foreign_key: { to_table: :letter_letters }, null: false
+      end
+      # rubocop:enable Rails/CreateTableWithTimestamps
+
+      add_index(
+        :letter_mailshot_items,
+        [:mailshot_id, :letter_id],
+        unique: true,
+        comment: "A sanity check that a letter appears only once in a mailshot"
+      )
+    end
+  end
+end

data/db/migrate/20200320103052_add_status_to_letter_mailshot_mailshots.rb

@@ -0,0 +1,14 @@
+class AddStatusToLetterMailshotMailshots < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_enum(
+        :background_job_status,
+        %w(queued processing success failure)
+      )
+      change_table :letter_mailshot_mailshots do |t|
+        t.enum :status, enum_name: :background_job_status
+        t.text :last_error
+      end
+    end
+  end
+end

data/db/migrate/20200401115705_add_label_abbrv_to_survey_questions.rb

@@ -0,0 +1,12 @@
+class AddLabelAbbrvToSurveyQuestions < ActiveRecord::Migration[5.2]
+  within_renalware_schema do
+    def change
+      add_column(
+        :survey_questions,
+        :label_abbrv,
+        :string,
+        comment: "If populated, used instead of label when displaying the table, to save space"
+      )
+    end
+  end
+end

data/db/migrate/20200408131217_associate_batch_with_ukrdc_transmission_log.rb

@@ -0,0 +1,15 @@
+class AssociateBatchWithUKRDCTransmissionLog < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      rename_table :ukrdc_batch_numbers, :ukrdc_batches
+      change_column_null :ukrdc_transmission_logs, :request_uuid, true
+      add_reference(
+        :ukrdc_transmission_logs,
+        :batch,
+        foreign_key: { to_table: :ukrdc_batches },
+        index: true,
+        null: true
+      )
+    end
+  end
+end